Module pipeline 

QSM pipeline stages and utilities

Shared stage functions that both qsmxt.rs and qsmbly call to ensure identical processing. Each consumer calls the stages individually with its own I/O and caching layer on top.

Pipeline stages (typical order)

0. run_motion_correction — optional: co-register the echo series before fitting across it
1. run_field_mapping — multi-echo phase → B0 field map (ppm)
2. run_bg_removal — total field → local field (ppm)
3. run_dipole_inversion — local field → susceptibility (ppm)
4. apply_reference — mean subtraction

Two-pass artefact reduction (two_pass) runs stages 2-3 a second time against a mask whose holes are intact, then folds the two reconstructions together.

per_echo runs stages 1-4 once per echo instead (QsmPipelineConfig::qsm_per_echo): a QSM for each echo, and their mean.

For TGV, use run_tgv which combines steps 1-4 internally.

run_qsmart reports its progress and intermediates (vessel mask, per-stage local fields and χ) to an Observer as borrowed slices, so a host can show or save them without the stage keeping copies.

rules says what each method requires, recommends and discourages of the rest of the configuration, with sources, and checks a configuration against it (rules::evaluate).

Combined algorithms

• HARPERELLA: SMV-based exterior Laplacian estimation (Li et al., 2014)
• iHARPERELLA: Phase-domain exterior estimation with improved low-freq suppression (Li et al., 2015)

Re-exports

pub use phase_utils::scale_phase_to_pi;

pub use phase_utils::hz_to_ppm;

pub use phase_utils::rads_to_ppm;

pub use phase_utils::ppm_to_hz;

pub use phase_utils::ppm_to_rads;

pub use phase_utils::rss_combine;

pub use referencing::apply_reference;

pub use masking::apply_mask_ops;

pub use masking::build_mask_section;

pub use masking::resolve_masking_input;

pub use masking::run_masking;

pub use masking::section_magnitude;

pub use motion::run_motion_correction;

pub use motion::MotionCorrectionConfig;

pub use motion::MotionCorrectionResult;

pub use field_mapping::run_field_mapping;

pub use bg_removal::run_bg_removal;

pub use inversion::heidi_seed_problem;

pub use inversion::run_dipole_inversion;

pub use inversion::run_heidi_cone_fill;

pub use inversion::run_tgv;

pub use inversion::run_nextqsm;

pub use inversion::run_iqsm;

pub use inversion::run_iqsm_plus;

pub use inversion::run_iqfm;

pub use separation::run_separation;

pub use separation::SeparationInputs;

pub use separation::SeparationResult;

pub use observer::Observer;

pub use observer::VolumeRef;

pub use qsmart::run_qsmart;

pub use two_pass::combine_two_pass;

pub use two_pass::default_reliable_sections;

pub use two_pass::restrict_reliable_mask;

pub use config::*;

Modules

bg_removal

Background field removal stage

config

Pipeline configuration types

field_mapping

Field mapping stage

inversion

Dipole inversion stage

masking

Masking stage

motion

Motion-correction stage: co-register a multi-echo series onto one echo before field mapping.

observer

Progress and intermediate outputs reported by pipeline stages as they run.

per_echo

Per-echo QSM: a susceptibility map reconstructed from each echo on its own.

phase_utils

Phase and field conversion utilities

qsmart

QSMART two-stage reconstruction

referencing

QSM referencing

rules

Pipeline rules: what each method requires, recommends and discourages, with sources.

separation

Susceptibility source-separation stage.

two_pass

Two-pass artefact reduction.